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Nature has evolved the ability to self-assemble molecules into functional architectures capable of specifically binding a diverse set of ligands. Our research program aspires to mimic aspects of this process by designing a set of peptide-based building blocks, which are multifaceted molecules conjugating elements that direct assembly to components that are responsible for specific binding interactions. Compared to ‘top-down’ approaches, such as lithography, programming molecules to self-assemble allows one to access complex structures in a parallel fashion, yielding faster kinetics for practical processing at nanometer length-scales. The design and application of such ‘bottom-up’ assemblies requires precision synthesis, predictive folding algorithms, and accurate characterization of self-assembly. This methodology is proving to be an effective tool for engineering drug delivery vehicles, biosensing, and molecular medicines.